Bug Summary

File:gromacs/gmxana/gmx_hydorder.c
Location:line 387, column 29
Description:Array access (from variable 'sk_4d') results in a null pointer dereference

Annotated Source Code

1/*
2 * This file is part of the GROMACS molecular simulation package.
3 *
4 * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6 * and including many others, as listed in the AUTHORS file in the
7 * top-level source directory and at http://www.gromacs.org.
8 *
9 * GROMACS is free software; you can redistribute it and/or
10 * modify it under the terms of the GNU Lesser General Public License
11 * as published by the Free Software Foundation; either version 2.1
12 * of the License, or (at your option) any later version.
13 *
14 * GROMACS is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 * Lesser General Public License for more details.
18 *
19 * You should have received a copy of the GNU Lesser General Public
20 * License along with GROMACS; if not, see
21 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
23 *
24 * If you want to redistribute modifications to GROMACS, please
25 * consider that scientific software is very special. Version
26 * control is crucial - bugs must be traceable. We will be happy to
27 * consider code for inclusion in the official distribution, but
28 * derived work must not be called official GROMACS. Details are found
29 * in the README & COPYING files - if they are missing, get the
30 * official version at http://www.gromacs.org.
31 *
32 * To help us fund GROMACS development, we humbly ask that you cite
33 * the research papers on the package. Check out http://www.gromacs.org.
34 */
35
36#ifdef HAVE_CONFIG_H1
37#include <config.h>
38#endif
39
40#include <math.h>
41#include <string.h>
42
43#include "typedefs.h"
44#include "gromacs/commandline/pargs.h"
45#include "gromacs/utility/smalloc.h"
46#include "macros.h"
47#include "gstat.h"
48#include "gromacs/math/vec.h"
49#include "gromacs/fileio/xvgr.h"
50#include "pbc.h"
51#include "gromacs/utility/futil.h"
52#include "index.h"
53#include "gromacs/fileio/tpxio.h"
54#include "gromacs/fileio/trxio.h"
55#include "gromacs/fileio/matio.h"
56#include "binsearch.h"
57#include "powerspect.h"
58
59#include "gromacs/utility/fatalerror.h"
60
61/* Print name of first atom in all groups in index file */
62static void print_types(atom_id index[], atom_id a[], int ngrps,
63 char *groups[], t_topology *top)
64{
65 int i;
66
67 fprintf(stderrstderr, "Using following groups: \n");
68 for (i = 0; i < ngrps; i++)
69 {
70 fprintf(stderrstderr, "Groupname: %s First atomname: %s First atomnr %u\n",
71 groups[i], *(top->atoms.atomname[a[index[i]]]), a[index[i]]);
72 }
73 fprintf(stderrstderr, "\n");
74}
75
76static void check_length(real length, int a, int b)
77{
78 if (length > 0.3)
79 {
80 fprintf(stderrstderr, "WARNING: distance between atoms %d and "
81 "%d > 0.3 nm (%f). Index file might be corrupt.\n",
82 a, b, length);
83 }
84}
85
86static void find_tetra_order_grid(t_topology top, int ePBC,
87 int natoms, matrix box,
88 rvec x[], int maxidx, atom_id index[],
89 real *sgmean, real *skmean,
90 int nslicex, int nslicey, int nslicez,
91 real ***sggrid, real ***skgrid)
92{
93 int ix, jx, i, j, k, l, n, *nn[4];
94 rvec dx, rj, rk, urk, urj;
95 real cost, cost2, *sgmol, *skmol, rmean, rmean2, r2, box2, *r_nn[4];
96 t_pbc pbc;
97 int slindex_x, slindex_y, slindex_z;
98 int ***sl_count;
99 real onethird = 1.0/3.0;
100 gmx_rmpbc_t gpbc;
101
102 /* dmat = init_mat(maxidx, FALSE); */
103
104 box2 = box[XX0][XX0] * box[XX0][XX0];
105
106 /* Initialize expanded sl_count array */
107 snew(sl_count, nslicex)(sl_count) = save_calloc("sl_count", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 107, (nslicex), sizeof(*(sl_count)));
108 for (i = 0; i < nslicex; i++)
109 {
110 snew(sl_count[i], nslicey)(sl_count[i]) = save_calloc("sl_count[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 110, (nslicey), sizeof(*(sl_count[i])));
111 for (j = 0; j < nslicey; j++)
112 {
113 snew(sl_count[i][j], nslicez)(sl_count[i][j]) = save_calloc("sl_count[i][j]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 113, (nslicez), sizeof(*(sl_count[i][j])));
114 }
115 }
116
117
118 for (i = 0; (i < 4); i++)
119 {
120 snew(r_nn[i], natoms)(r_nn[i]) = save_calloc("r_nn[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 120, (natoms), sizeof(*(r_nn[i])));
121 snew(nn[i], natoms)(nn[i]) = save_calloc("nn[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 121, (natoms), sizeof(*(nn[i])));
122
123 for (j = 0; (j < natoms); j++)
124 {
125 r_nn[i][j] = box2;
126 }
127 }
128
129 snew(sgmol, maxidx)(sgmol) = save_calloc("sgmol", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 129, (maxidx), sizeof(*(sgmol)));
130 snew(skmol, maxidx)(skmol) = save_calloc("skmol", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 130, (maxidx), sizeof(*(skmol)));
131
132 /* Must init pbc every step because of pressure coupling */
133 set_pbc(&pbc, ePBC, box);
134 gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
135 gmx_rmpbc(gpbc, natoms, box, x);
136
137 *sgmean = 0.0;
138 *skmean = 0.0;
139 l = 0;
140 for (i = 0; (i < maxidx); i++)
141 { /* loop over index file */
142 ix = index[i];
143 for (j = 0; (j < maxidx); j++)
144 {
145
146 if (i == j)
147 {
148 continue;
149 }
150
151 jx = index[j];
152
153 pbc_dx(&pbc, x[ix], x[jx], dx);
154 r2 = iprod(dx, dx);
155
156 /* set_mat_entry(dmat,i,j,r2); */
157
158 /* determine the nearest neighbours */
159 if (r2 < r_nn[0][i])
160 {
161 r_nn[3][i] = r_nn[2][i]; nn[3][i] = nn[2][i];
162 r_nn[2][i] = r_nn[1][i]; nn[2][i] = nn[1][i];
163 r_nn[1][i] = r_nn[0][i]; nn[1][i] = nn[0][i];
164 r_nn[0][i] = r2; nn[0][i] = j;
165 }
166 else if (r2 < r_nn[1][i])
167 {
168 r_nn[3][i] = r_nn[2][i]; nn[3][i] = nn[2][i];
169 r_nn[2][i] = r_nn[1][i]; nn[2][i] = nn[1][i];
170 r_nn[1][i] = r2; nn[1][i] = j;
171 }
172 else if (r2 < r_nn[2][i])
173 {
174 r_nn[3][i] = r_nn[2][i]; nn[3][i] = nn[2][i];
175 r_nn[2][i] = r2; nn[2][i] = j;
176 }
177 else if (r2 < r_nn[3][i])
178 {
179 r_nn[3][i] = r2; nn[3][i] = j;
180 }
181 }
182
183
184 /* calculate mean distance between nearest neighbours */
185 rmean = 0;
186 for (j = 0; (j < 4); j++)
187 {
188 r_nn[j][i] = sqrt(r_nn[j][i]);
189 rmean += r_nn[j][i];
190 }
191 rmean /= 4;
192
193 n = 0;
194 sgmol[i] = 0.0;
195 skmol[i] = 0.0;
196
197 /* Chau1998a eqn 3 */
198 /* angular part tetrahedrality order parameter per atom */
199 for (j = 0; (j < 3); j++)
200 {
201 for (k = j+1; (k < 4); k++)
202 {
203 pbc_dx(&pbc, x[ix], x[index[nn[k][i]]], rk);
204 pbc_dx(&pbc, x[ix], x[index[nn[j][i]]], rj);
205
206 unitv(rk, urk);
207 unitv(rj, urj);
208
209 cost = iprod(urk, urj) + onethird;
210 cost2 = cost * cost;
211
212 sgmol[i] += cost2;
213 l++;
214 n++;
215 }
216 }
217 /* normalize sgmol between 0.0 and 1.0 */
218 sgmol[i] = 3*sgmol[i]/32;
219 *sgmean += sgmol[i];
220
221 /* distance part tetrahedrality order parameter per atom */
222 rmean2 = 4 * 3 * rmean * rmean;
223 for (j = 0; (j < 4); j++)
224 {
225 skmol[i] += (rmean - r_nn[j][i]) * (rmean - r_nn[j][i]) / rmean2;
226 /* printf("%d %f (%f %f %f %f) \n",
227 i, skmol[i], rmean, rmean2, r_nn[j][i], (rmean - r_nn[j][i]) );
228 */
229 }
230
231 *skmean += skmol[i];
232
233 /* Compute sliced stuff in x y z*/
234 slindex_x = gmx_nint((1+x[i][XX0]/box[XX0][XX0])*nslicex) % nslicex;
235 slindex_y = gmx_nint((1+x[i][YY1]/box[YY1][YY1])*nslicey) % nslicey;
236 slindex_z = gmx_nint((1+x[i][ZZ2]/box[ZZ2][ZZ2])*nslicez) % nslicez;
237 sggrid[slindex_x][slindex_y][slindex_z] += sgmol[i];
238 skgrid[slindex_x][slindex_y][slindex_z] += skmol[i];
239 (sl_count[slindex_x][slindex_y][slindex_z])++;
240 } /* loop over entries in index file */
241
242 *sgmean /= maxidx;
243 *skmean /= maxidx;
244
245 for (i = 0; (i < nslicex); i++)
246 {
247 for (j = 0; j < nslicey; j++)
248 {
249 for (k = 0; k < nslicez; k++)
250 {
251 if (sl_count[i][j][k] > 0)
252 {
253 sggrid[i][j][k] /= sl_count[i][j][k];
254 skgrid[i][j][k] /= sl_count[i][j][k];
255 }
256 }
257 }
258 }
259
260 sfree(sl_count)save_free("sl_count", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 260, (sl_count));
261 sfree(sgmol)save_free("sgmol", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 261, (sgmol));
262 sfree(skmol)save_free("skmol", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 262, (skmol));
263 for (i = 0; (i < 4); i++)
264 {
265 sfree(r_nn[i])save_free("r_nn[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 265, (r_nn[i]));
266 sfree(nn[i])save_free("nn[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 266, (nn[i]));
267 }
268}
269
270/*Determines interface from tetrahedral order parameter in box with specified binwidth. */
271/*Outputs interface positions(bins), the number of timeframes, and the number of surface-mesh points in xy*/
272
273static void calc_tetra_order_interface(const char *fnNDX, const char *fnTPS, const char *fnTRX, real binw, int tblock,
274 int *nframes, int *nslicex, int *nslicey,
275 real sgang1, real sgang2, real ****intfpos,
276 output_env_t oenv)
277{
278 FILE *fpsg = NULL((void*)0), *fpsk = NULL((void*)0);
279 char *sgslfn = "sg_ang_mesh"; /* Hardcoded filenames for debugging*/
280 char *skslfn = "sk_dist_mesh";
281 t_topology top;
282 int ePBC;
283 char title[STRLEN4096], subtitle[STRLEN4096];
284 t_trxstatus *status;
285 int natoms;
286 real t;
287 rvec *xtop, *x;
288 matrix box;
289 real sg, sk, sgintf, pos;
290 atom_id **index = NULL((void*)0);
291 char **grpname = NULL((void*)0);
292 int i, j, k, n, *isize, ng, nslicez, framenr;
293 real ***sg_grid = NULL((void*)0), ***sk_grid = NULL((void*)0), ***sg_fravg = NULL((void*)0), ***sk_fravg = NULL((void*)0), ****sk_4d = NULL((void*)0), ****sg_4d = NULL((void*)0);
294 int *perm;
295 int ndx1, ndx2;
296 int bins;
297 const real onehalf = 1.0/2.0;
298 /* real ***intfpos[2]; pointers to arrays of two interface positions zcoord(framenr,xbin,ybin): intfpos[interface_index][t][nslicey*x+y]
299 * i.e 1D Row-major order in (t,x,y) */
300
301
302 read_tps_conf(fnTPS, title, &top, &ePBC, &xtop, NULL((void*)0), box, FALSE0);
303
304 *nslicex = (int)(box[XX0][XX0]/binw + onehalf); /*Calculate slicenr from binwidth*/
305 *nslicey = (int)(box[YY1][YY1]/binw + onehalf);
306 nslicez = (int)(box[ZZ2][ZZ2]/binw + onehalf);
307
308
309
310 ng = 1;
311 /* get index groups */
312 printf("Select the group that contains the atoms you want to use for the tetrahedrality order parameter calculation:\n");
313 snew(grpname, ng)(grpname) = save_calloc("grpname", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 313, (ng), sizeof(*(grpname)));
314 snew(index, ng)(index) = save_calloc("index", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 314, (ng), sizeof(*(index)));
315 snew(isize, ng)(isize) = save_calloc("isize", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 315, (ng), sizeof(*(isize)));
316 get_index(&top.atoms, fnNDX, ng, isize, index, grpname);
317
318 /* Analyze trajectory */
319 natoms = read_first_x(oenv, &status, fnTRX, &t, &x, box);
320 if (natoms > top.atoms.nr)
1
Taking false branch
→
321 {
322 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 322, "Topology (%d atoms) does not match trajectory (%d atoms)",
323 top.atoms.nr, natoms);
324 }
325 check_index(NULL((void*)0), ng, index[0], NULL((void*)0), natoms);
326
327
328 /*Prepare structures for temporary storage of frame info*/
329 snew(sg_grid, *nslicex)(sg_grid) = save_calloc("sg_grid", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 329, (*nslicex), sizeof(*(sg_grid)));
330 snew(sk_grid, *nslicex)(sk_grid) = save_calloc("sk_grid", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 330, (*nslicex), sizeof(*(sk_grid)));
331 for (i = 0; i < *nslicex; i++)
2
←
Loop condition is false. Execution continues on line 342
→
332 {
333 snew(sg_grid[i], *nslicey)(sg_grid[i]) = save_calloc("sg_grid[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 333, (*nslicey), sizeof(*(sg_grid[i])));
334 snew(sk_grid[i], *nslicey)(sk_grid[i]) = save_calloc("sk_grid[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 334, (*nslicey), sizeof(*(sk_grid[i])));
335 for (j = 0; j < *nslicey; j++)
336 {
337 snew(sg_grid[i][j], nslicez)(sg_grid[i][j]) = save_calloc("sg_grid[i][j]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 337, (nslicez), sizeof(*(sg_grid[i][j])));
338 snew(sk_grid[i][j], nslicez)(sk_grid[i][j]) = save_calloc("sk_grid[i][j]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 338, (nslicez), sizeof(*(sk_grid[i][j])));
339 }
340 }
341
342 sg_4d = NULL((void*)0);
343 sk_4d = NULL((void*)0);
3
←
Null pointer value stored to 'sk_4d'
→
344 *nframes = 0;
345 framenr = 0;
346
347/* Loop over frames*/
348 do
349 {
350 /*Initialize box meshes (temporary storage for each tblock frame -reinitialise every tblock steps */
351 if (framenr%tblock == 0)
4
←
Taking false branch
→
352 {
353 srenew(sk_4d, *nframes+1)(sk_4d) = save_realloc("sk_4d", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 353, (sk_4d), (*nframes+1), sizeof(*(sk_4d)));
354 srenew(sg_4d, *nframes+1)(sg_4d) = save_realloc("sg_4d", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 354, (sg_4d), (*nframes+1), sizeof(*(sg_4d)));
355 snew(sg_fravg, *nslicex)(sg_fravg) = save_calloc("sg_fravg", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 355, (*nslicex), sizeof(*(sg_fravg)));
356 snew(sk_fravg, *nslicex)(sk_fravg) = save_calloc("sk_fravg", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 356, (*nslicex), sizeof(*(sk_fravg)));
357 for (i = 0; i < *nslicex; i++)
358 {
359 snew(sg_fravg[i], *nslicey)(sg_fravg[i]) = save_calloc("sg_fravg[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 359, (*nslicey), sizeof(*(sg_fravg[i])));
360 snew(sk_fravg[i], *nslicey)(sk_fravg[i]) = save_calloc("sk_fravg[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 360, (*nslicey), sizeof(*(sk_fravg[i])));
361 for (j = 0; j < *nslicey; j++)
362 {
363 snew(sg_fravg[i][j], nslicez)(sg_fravg[i][j]) = save_calloc("sg_fravg[i][j]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 363, (nslicez), sizeof(*(sg_fravg[i][j])));
364 snew(sk_fravg[i][j], nslicez)(sk_fravg[i][j]) = save_calloc("sk_fravg[i][j]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 364, (nslicez), sizeof(*(sk_fravg[i][j])));
365 }
366 }
367 }
368
369 find_tetra_order_grid(top, ePBC, natoms, box, x, isize[0], index[0],
370 &sg, &sk, *nslicex, *nslicey, nslicez, sg_grid, sk_grid);
371 for (i = 0; i < *nslicex; i++)
5
←
Loop condition is false. Execution continues on line 383
→
372 {
373 for (j = 0; j < *nslicey; j++)
374 {
375 for (k = 0; k < nslicez; k++)
376 {
377 sk_fravg[i][j][k] += sk_grid[i][j][k]/tblock;
378 sg_fravg[i][j][k] += sg_grid[i][j][k]/tblock;
379 }
380 }
381 }
382
383 framenr++;
384
385 if (framenr%tblock == 0)
6
←
Taking true branch
→
386 {
387 sk_4d[*nframes] = sk_fravg;
7
←
Array access (from variable 'sk_4d') results in a null pointer dereference
388 sg_4d[*nframes] = sg_fravg;
389 (*nframes)++;
390 }
391
392 }
393 while (read_next_x(oenv, status, &t, x, box));
394 close_trj(status);
395
396 sfree(grpname)save_free("grpname", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 396, (grpname));
397 sfree(index)save_free("index", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 397, (index));
398 sfree(isize)save_free("isize", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 398, (isize));
399
400 /*Debugging for printing out the entire order parameter meshes.*/
401 if (debug)
402 {
403 fpsg = xvgropen(sgslfn, "S\\sg\\N Angle Order Parameter / Meshpoint", "(nm)", "S\\sg\\N", oenv);
404 fpsk = xvgropen(skslfn, "S\\sk\\N Distance Order Parameter / Meshpoint", "(nm)", "S\\sk\\N", oenv);
405 for (n = 0; n < (*nframes); n++)
406 {
407 fprintf(fpsg, "%i\n", n);
408 fprintf(fpsk, "%i\n", n);
409 for (i = 0; (i < *nslicex); i++)
410 {
411 for (j = 0; j < *nslicey; j++)
412 {
413 for (k = 0; k < nslicez; k++)
414 {
415 fprintf(fpsg, "%4f %4f %4f %8f\n", (i+0.5)*box[XX0][XX0]/(*nslicex), (j+0.5)*box[YY1][YY1]/(*nslicey), (k+0.5)*box[ZZ2][ZZ2]/nslicez, sg_4d[n][i][j][k]);
416 fprintf(fpsk, "%4f %4f %4f %8f\n", (i+0.5)*box[XX0][XX0]/(*nslicex), (j+0.5)*box[YY1][YY1]/(*nslicey), (k+0.5)*box[ZZ2][ZZ2]/nslicez, sk_4d[n][i][j][k]);
417 }
418 }
419 }
420 }
421 xvgrclose(fpsg);
422 xvgrclose(fpsk);
423 }
424
425
426 /* Find positions of interface z by scanning orderparam for each frame and for each xy-mesh cylinder along z*/
427
428 /*Simple trial: assume interface is in the middle of -sgang1 and sgang2*/
429 sgintf = 0.5*(sgang1+sgang2);
430
431
432 /*Allocate memory for interface arrays; */
433 snew((*intfpos), 2)((*intfpos)) = save_calloc("(*intfpos)", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 433, (2), sizeof(*((*intfpos))));
434 snew((*intfpos)[0], *nframes)((*intfpos)[0]) = save_calloc("(*intfpos)[0]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 434, (*nframes), sizeof(*((*intfpos)[0])));
435 snew((*intfpos)[1], *nframes)((*intfpos)[1]) = save_calloc("(*intfpos)[1]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 435, (*nframes), sizeof(*((*intfpos)[1])));
436
437 bins = (*nslicex)*(*nslicey);
438
439
440 snew(perm, nslicez)(perm) = save_calloc("perm", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 440, (nslicez), sizeof(*(perm))); /*permutation array for sorting along normal coordinate*/
441
442
443 for (n = 0; n < *nframes; n++)
444 {
445 snew((*intfpos)[0][n], bins)((*intfpos)[0][n]) = save_calloc("(*intfpos)[0][n]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 445, (bins), sizeof(*((*intfpos)[0][n])));
446 snew((*intfpos)[1][n], bins)((*intfpos)[1][n]) = save_calloc("(*intfpos)[1][n]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 446, (bins), sizeof(*((*intfpos)[1][n])));
447 for (i = 0; i < *nslicex; i++)
448 {
449 for (j = 0; j < *nslicey; j++)
450 {
451 rangeArray(perm, nslicez); /*reset permutation array to identity*/
452 /*Binsearch returns 2 bin-numbers where the order param is <= setpoint sgintf*/
453 ndx1 = start_binsearch(sg_4d[n][i][j], perm, 0, nslicez/2-1, sgintf, 1);
454 ndx2 = start_binsearch(sg_4d[n][i][j], perm, nslicez/2, nslicez-1, sgintf, -1);
455 /*Use linear interpolation to smooth out the interface position*/
456
457 /*left interface (0)*/
458 /*if((sg_4d[n][i][j][perm[ndx1+1]]-sg_4d[n][i][j][perm[ndx1]])/sg_4d[n][i][j][perm[ndx1]] > 0.01){
459 pos=( (sgintf-sg_4d[n][i][j][perm[ndx1]])*perm[ndx1+1]+(sg_4d[n][i][j][perm[ndx1+1]]-sgintf)*perm[ndx1 ])*/
460 (*intfpos)[0][n][j+*nslicey*i] = (perm[ndx1]+onehalf)*binw;
461 /*right interface (1)*/
462 /*alpha=(sgintf-sg_4d[n][i][j][perm[ndx2]])/(sg_4d[n][i][j][perm[ndx2]+1]-sg_4d[n][i][j][perm[ndx2]]);*/
463 /*(*intfpos)[1][n][j+*nslicey*i]=((1-alpha)*perm[ndx2]+alpha*(perm[ndx2]+1)+onehalf)*box[ZZ][ZZ]/nslicez;*/
464 (*intfpos)[1][n][j+*nslicey*i] = (perm[ndx2]+onehalf)*binw;
465 }
466 }
467 }
468
469
470 /*sfree(perm);*/
471 sfree(sk_4d)save_free("sk_4d", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 471, (sk_4d));
472 sfree(sg_4d)save_free("sg_4d", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 472, (sg_4d));
473 /*sfree(sg_grid);*/
474 /*sfree(sk_grid);*/
475
476
477}
478
479static void writesurftoxpms(real ***surf, int tblocks, int xbins, int ybins, real bw, char **outfiles, int maplevels )
480{
481
482 char numbuf[8];
483 int n, i, j;
484 real **profile1, **profile2;
485 real max1, max2, min1, min2, *xticks, *yticks;
486 t_rgb lo = {1, 1, 1};
487 t_rgb hi = {0, 0, 0};
488 FILE *xpmfile1, *xpmfile2;
489
490/*Prepare xpm structures for output*/
491
492/*Allocate memory to tick's and matrices*/
493 snew (xticks, xbins+1)(xticks) = save_calloc("xticks", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 493, (xbins+1), sizeof(*(xticks)));
494 snew (yticks, ybins+1)(yticks) = save_calloc("yticks", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 494, (ybins+1), sizeof(*(yticks)));
495
496 profile1 = mk_matrix(xbins, ybins, FALSE0);
497 profile2 = mk_matrix(xbins, ybins, FALSE0);
498
499 for (i = 0; i < xbins+1; i++)
500 {
501 xticks[i] += bw;
502 }
503 for (j = 0; j < ybins+1; j++)
504 {
505 yticks[j] += bw;
506 }
507
508 xpmfile1 = gmx_ffopen(outfiles[0], "w");
509 xpmfile2 = gmx_ffopen(outfiles[1], "w");
510
511 max1 = max2 = 0.0;
512 min1 = min2 = 1000.00;
513
514 for (n = 0; n < tblocks; n++)
515 {
516 sprintf(numbuf, "%5d", n);
517 /*Filling matrices for inclusion in xpm-files*/
518 for (i = 0; i < xbins; i++)
519 {
520 for (j = 0; j < ybins; j++)
521 {
522 profile1[i][j] = (surf[0][n][j+ybins*i]);
523 profile2[i][j] = (surf[1][n][j+ybins*i]);
524 /*Finding max and min values*/
525 if (profile1[i][j] > max1)
526 {
527 max1 = profile1[i][j];
528 }
529 if (profile1[i][j] < min1)
530 {
531 min1 = profile1[i][j];
532 }
533 if (profile2[i][j] > max2)
534 {
535 max2 = profile2[i][j];
536 }
537 if (profile2[i][j] < min2)
538 {
539 min2 = profile2[i][j];
540 }
541 }
542 }
543
544 write_xpm(xpmfile1, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks, profile1, min1, max1, lo, hi, &maplevels);
545 write_xpm(xpmfile2, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks, profile2, min2, max2, lo, hi, &maplevels);
546 }
547
548 gmx_ffclose(xpmfile1);
549 gmx_ffclose(xpmfile2);
550
551
552
553 sfree(profile1)save_free("profile1", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 553, (profile1));
554 sfree(profile2)save_free("profile2", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 554, (profile2));
555 sfree(xticks)save_free("xticks", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 555, (xticks));
556 sfree(yticks)save_free("yticks", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 556, (yticks));
557}
558
559
560static void writeraw(real ***surf, int tblocks, int xbins, int ybins, char **fnms)
561{
562 FILE *raw1, *raw2;
563 int i, j, n;
564
565 raw1 = gmx_ffopen(fnms[0], "w");
566 raw2 = gmx_ffopen(fnms[1], "w");
567 fprintf(raw1, "#Legend\n#TBlock\n#Xbin Ybin Z t\n");
568 fprintf(raw2, "#Legend\n#TBlock\n#Xbin Ybin Z t\n");
569 for (n = 0; n < tblocks; n++)
570 {
571 fprintf(raw1, "%5d\n", n);
572 fprintf(raw2, "%5d\n", n);
573 for (i = 0; i < xbins; i++)
574 {
575 for (j = 0; j < ybins; j++)
576 {
577 fprintf(raw1, "%i %i %8.5f\n", i, j, (surf[0][n][j+ybins*i]));
578 fprintf(raw2, "%i %i %8.5f\n", i, j, (surf[1][n][j+ybins*i]));
579 }
580 }
581 }
582
583 gmx_ffclose(raw1);
584 gmx_ffclose(raw2);
585}
586
587
588
589int gmx_hydorder(int argc, char *argv[])
590{
591 static const char *desc[] = {
592 "[THISMODULE] computes the tetrahedrality order parameters around a ",
593 "given atom. Both angle an distance order parameters are calculated. See",
594 "P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.",
595 "for more details.[PAR]"
596 "[THISMODULE] calculates the order parameter in a 3d-mesh in the box, and",
597 "with 2 phases in the box gives the user the option to define a 2D interface in time",
598 "separating the faces by specifying parameters [TT]-sgang1[tt] and",
599 "[TT]-sgang2[tt] (it is important to select these judiciously)."
600 };
601
602 int axis = 0;
603 static int nsttblock = 1;
604 static int nlevels = 100;
605 static real binwidth = 1.0; /* binwidth in mesh */
606 static real sg1 = 1;
607 static real sg2 = 1; /* order parameters for bulk phases */
608 static gmx_bool bFourier = FALSE0;
609 static gmx_bool bRawOut = FALSE0;
610 int frames, xslices, yslices; /* Dimensions of interface arrays*/
611 real ***intfpos; /* Interface arrays (intfnr,t,xy) -potentially large */
612 static char *normal_axis[] = { NULL((void*)0), "z", "x", "y", NULL((void*)0) };
613
614 t_pargs pa[] = {
615 { "-d", FALSE0, etENUM, {normal_axis},
616 "Direction of the normal on the membrane" },
617 { "-bw", FALSE0, etREAL, {&binwidth},
618 "Binwidth of box mesh" },
619 { "-sgang1", FALSE0, etREAL, {&sg1},
620 "tetrahedral angle parameter in Phase 1 (bulk)" },
621 { "-sgang2", FALSE0, etREAL, {&sg2},
622 "tetrahedral angle parameter in Phase 2 (bulk)" },
623 { "-tblock", FALSE0, etINT, {&nsttblock},
624 "Number of frames in one time-block average"},
625 { "-nlevel", FALSE0, etINT, {&nlevels},
626 "Number of Height levels in 2D - XPixMaps"}
627 };
628
629 t_filenm fnm[] = { /* files for g_order */
630 { efTRX, "-f", NULL((void*)0), ffREAD1<<1 }, /* trajectory file */
631 { efNDX, "-n", NULL((void*)0), ffREAD1<<1 }, /* index file */
632 { efTPX, "-s", NULL((void*)0), ffREAD1<<1 }, /* topology file */
633 { efXPM, "-o", "intf", ffWRMULT(1<<2 | 1<<5)}, /* XPM- surface maps */
634 { efOUT, "-or", "raw", ffOPTWRMULT((1<<2 | 1<<5) | 1<<3) }, /* xvgr output file */
635 { efOUT, "-Spect", "intfspect", ffOPTWRMULT((1<<2 | 1<<5) | 1<<3)}, /* Fourier spectrum interfaces */
636 };
637#define NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))) asize(fnm)((int)(sizeof(fnm)/sizeof((fnm)[0])))
638
639 /*Filenames*/
640 const char *ndxfnm, *tpsfnm, *trxfnm;
641 char **spectra, **intfn, **raw;
642 int nfspect, nfxpm, nfraw;
643 output_env_t oenv;
644
645 if (!parse_common_args(&argc, argv, PCA_CAN_VIEW(1<<5) | PCA_CAN_TIME((1<<6) | (1<<7) | (1<<14)) | PCA_BE_NICE(1<<13),
646 NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm, asize(pa)((int)(sizeof(pa)/sizeof((pa)[0]))), pa, asize(desc)((int)(sizeof(desc)/sizeof((desc)[0]))), desc, 0, NULL((void*)0), &oenv))
647 {
648 return 0;
649 }
650 bFourier = opt2bSet("-Spect", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
651 bRawOut = opt2bSet("-or", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
652
653 if (binwidth < 0.0)
654 {
655 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 655, "Can not have binwidth < 0");
656 }
657
658 ndxfnm = ftp2fn(efNDX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
659 tpsfnm = ftp2fn(efTPX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
660 trxfnm = ftp2fn(efTRX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
661
662 /* Calculate axis */
663 if (strcmp(normal_axis[0], "x")__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p
(normal_axis[0]) && __builtin_constant_p ("x") &&
(__s1_len = strlen (normal_axis[0]), __s2_len = strlen ("x")
, (!((size_t)(const void *)((normal_axis[0]) + 1) - (size_t)(
const void *)(normal_axis[0]) == 1) || __s1_len >= 4) &&
(!((size_t)(const void *)(("x") + 1) - (size_t)(const void *
)("x") == 1) || __s2_len >= 4)) ? __builtin_strcmp (normal_axis
[0], "x") : (__builtin_constant_p (normal_axis[0]) &&
((size_t)(const void *)((normal_axis[0]) + 1) - (size_t)(const
void *)(normal_axis[0]) == 1) && (__s1_len = strlen (
normal_axis[0]), __s1_len < 4) ? (__builtin_constant_p ("x"
) && ((size_t)(const void *)(("x") + 1) - (size_t)(const
void *)("x") == 1) ? __builtin_strcmp (normal_axis[0], "x") :
(__extension__ ({ const unsigned char *__s2 = (const unsigned
char *) (const char *) ("x"); int __result = (((const unsigned
char *) (const char *) (normal_axis[0]))[0] - __s2[0]); if (
__s1_len > 0 && __result == 0) { __result = (((const
unsigned char *) (const char *) (normal_axis[0]))[1] - __s2[
1]); if (__s1_len > 1 && __result == 0) { __result
= (((const unsigned char *) (const char *) (normal_axis[0]))
[2] - __s2[2]); if (__s1_len > 2 && __result == 0)
__result = (((const unsigned char *) (const char *) (normal_axis
[0]))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p
("x") && ((size_t)(const void *)(("x") + 1) - (size_t
)(const void *)("x") == 1) && (__s2_len = strlen ("x"
), __s2_len < 4) ? (__builtin_constant_p (normal_axis[0]) &&
((size_t)(const void *)((normal_axis[0]) + 1) - (size_t)(const
void *)(normal_axis[0]) == 1) ? __builtin_strcmp (normal_axis
[0], "x") : (- (__extension__ ({ const unsigned char *__s2 = (
const unsigned char *) (const char *) (normal_axis[0]); int __result
= (((const unsigned char *) (const char *) ("x"))[0] - __s2[
0]); if (__s2_len > 0 && __result == 0) { __result
= (((const unsigned char *) (const char *) ("x"))[1] - __s2[
1]); if (__s2_len > 1 && __result == 0) { __result
= (((const unsigned char *) (const char *) ("x"))[2] - __s2[
2]); if (__s2_len > 2 && __result == 0) __result =
(((const unsigned char *) (const char *) ("x"))[3] - __s2[3]
); } } __result; })))) : __builtin_strcmp (normal_axis[0], "x"
)))); }) == 0)
664 {
665 axis = XX0;
666 }
667 else if (strcmp(normal_axis[0], "y")__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p
(normal_axis[0]) && __builtin_constant_p ("y") &&
(__s1_len = strlen (normal_axis[0]), __s2_len = strlen ("y")
, (!((size_t)(const void *)((normal_axis[0]) + 1) - (size_t)(
const void *)(normal_axis[0]) == 1) || __s1_len >= 4) &&
(!((size_t)(const void *)(("y") + 1) - (size_t)(const void *
)("y") == 1) || __s2_len >= 4)) ? __builtin_strcmp (normal_axis
[0], "y") : (__builtin_constant_p (normal_axis[0]) &&
((size_t)(const void *)((normal_axis[0]) + 1) - (size_t)(const
void *)(normal_axis[0]) == 1) && (__s1_len = strlen (
normal_axis[0]), __s1_len < 4) ? (__builtin_constant_p ("y"
) && ((size_t)(const void *)(("y") + 1) - (size_t)(const
void *)("y") == 1) ? __builtin_strcmp (normal_axis[0], "y") :
(__extension__ ({ const unsigned char *__s2 = (const unsigned
char *) (const char *) ("y"); int __result = (((const unsigned
char *) (const char *) (normal_axis[0]))[0] - __s2[0]); if (
__s1_len > 0 && __result == 0) { __result = (((const
unsigned char *) (const char *) (normal_axis[0]))[1] - __s2[
1]); if (__s1_len > 1 && __result == 0) { __result
= (((const unsigned char *) (const char *) (normal_axis[0]))
[2] - __s2[2]); if (__s1_len > 2 && __result == 0)
__result = (((const unsigned char *) (const char *) (normal_axis
[0]))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p
("y") && ((size_t)(const void *)(("y") + 1) - (size_t
)(const void *)("y") == 1) && (__s2_len = strlen ("y"
), __s2_len < 4) ? (__builtin_constant_p (normal_axis[0]) &&
((size_t)(const void *)((normal_axis[0]) + 1) - (size_t)(const
void *)(normal_axis[0]) == 1) ? __builtin_strcmp (normal_axis
[0], "y") : (- (__extension__ ({ const unsigned char *__s2 = (
const unsigned char *) (const char *) (normal_axis[0]); int __result
= (((const unsigned char *) (const char *) ("y"))[0] - __s2[
0]); if (__s2_len > 0 && __result == 0) { __result
= (((const unsigned char *) (const char *) ("y"))[1] - __s2[
1]); if (__s2_len > 1 && __result == 0) { __result
= (((const unsigned char *) (const char *) ("y"))[2] - __s2[
2]); if (__s2_len > 2 && __result == 0) __result =
(((const unsigned char *) (const char *) ("y"))[3] - __s2[3]
); } } __result; })))) : __builtin_strcmp (normal_axis[0], "y"
)))); }) == 0)
668 {
669 axis = YY1;
670 }
671 else if (strcmp(normal_axis[0], "z")__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p
(normal_axis[0]) && __builtin_constant_p ("z") &&
(__s1_len = strlen (normal_axis[0]), __s2_len = strlen ("z")
, (!((size_t)(const void *)((normal_axis[0]) + 1) - (size_t)(
const void *)(normal_axis[0]) == 1) || __s1_len >= 4) &&
(!((size_t)(const void *)(("z") + 1) - (size_t)(const void *
)("z") == 1) || __s2_len >= 4)) ? __builtin_strcmp (normal_axis
[0], "z") : (__builtin_constant_p (normal_axis[0]) &&
((size_t)(const void *)((normal_axis[0]) + 1) - (size_t)(const
void *)(normal_axis[0]) == 1) && (__s1_len = strlen (
normal_axis[0]), __s1_len < 4) ? (__builtin_constant_p ("z"
) && ((size_t)(const void *)(("z") + 1) - (size_t)(const
void *)("z") == 1) ? __builtin_strcmp (normal_axis[0], "z") :
(__extension__ ({ const unsigned char *__s2 = (const unsigned
char *) (const char *) ("z"); int __result = (((const unsigned
char *) (const char *) (normal_axis[0]))[0] - __s2[0]); if (
__s1_len > 0 && __result == 0) { __result = (((const
unsigned char *) (const char *) (normal_axis[0]))[1] - __s2[
1]); if (__s1_len > 1 && __result == 0) { __result
= (((const unsigned char *) (const char *) (normal_axis[0]))
[2] - __s2[2]); if (__s1_len > 2 && __result == 0)
__result = (((const unsigned char *) (const char *) (normal_axis
[0]))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p
("z") && ((size_t)(const void *)(("z") + 1) - (size_t
)(const void *)("z") == 1) && (__s2_len = strlen ("z"
), __s2_len < 4) ? (__builtin_constant_p (normal_axis[0]) &&
((size_t)(const void *)((normal_axis[0]) + 1) - (size_t)(const
void *)(normal_axis[0]) == 1) ? __builtin_strcmp (normal_axis
[0], "z") : (- (__extension__ ({ const unsigned char *__s2 = (
const unsigned char *) (const char *) (normal_axis[0]); int __result
= (((const unsigned char *) (const char *) ("z"))[0] - __s2[
0]); if (__s2_len > 0 && __result == 0) { __result
= (((const unsigned char *) (const char *) ("z"))[1] - __s2[
1]); if (__s2_len > 1 && __result == 0) { __result
= (((const unsigned char *) (const char *) ("z"))[2] - __s2[
2]); if (__s2_len > 2 && __result == 0) __result =
(((const unsigned char *) (const char *) ("z"))[3] - __s2[3]
); } } __result; })))) : __builtin_strcmp (normal_axis[0], "z"
)))); }) == 0)
672 {
673 axis = ZZ2;
674 }
675 else
676 {
677 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 677, "Invalid axis, use x, y or z");
678 }
679
680 switch (axis)
681 {
682 case 0:
683 fprintf(stderrstderr, "Taking x axis as normal to the membrane\n");
684 break;
685 case 1:
686 fprintf(stderrstderr, "Taking y axis as normal to the membrane\n");
687 break;
688 case 2:
689 fprintf(stderrstderr, "Taking z axis as normal to the membrane\n");
690 break;
691 }
692
693 /* tetraheder order parameter */
694 /* If either of the options is set we compute both */
695 nfxpm = opt2fns(&intfn, "-o", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
696 if (nfxpm != 2)
697 {
698 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 698, "No or not correct number (2) of output-files: %d", nfxpm);
699 }
700 calc_tetra_order_interface(ndxfnm, tpsfnm, trxfnm, binwidth, nsttblock, &frames, &xslices, &yslices, sg1, sg2, &intfpos, oenv);
701 writesurftoxpms(intfpos, frames, xslices, yslices, binwidth, intfn, nlevels);
702
703 if (bFourier)
704 {
705 nfspect = opt2fns(&spectra, "-Spect", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
706 if (nfspect != 2)
707 {
708 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 708, "No or not correct number (2) of output-files: %d", nfspect);
709 }
710 powerspectavg(intfpos, frames, xslices, yslices, spectra);
711 }
712
713 if (bRawOut)
714 {
715 nfraw = opt2fns(&raw, "-or", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
716 if (nfraw != 2)
717 {
718 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_hydorder.c"
, 718, "No or not correct number (2) of output-files: %d", nfraw);
719 }
720 writeraw(intfpos, frames, xslices, yslices, raw);
721 }
722
723 return 0;
724}